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Human Phenotype Ontology Workbench

Home Page: http://hpo-workbench.readthedocs.io/en/latest/

License: BSD 3-Clause "New" or "Revised" License

Java 97.87% CSS 0.62% Shell 1.50%

hpoworkbench's Introduction

Documentation Status Codacy Badge

HPO Workbench

A Java app for working with the Human Phenotype Ontology (HPO).

A Java app for working with HPO and HPO annotation data. HPO Workbench can be used to get an overview of the HPO by navigating through the hierarchy and displaying the term definition etc.

Please see the full documentation.

Version 2

We are working on a version 2 using Java 17 and Spring Boot. To run HPO Workbench, you will need to have Java 16 and maven installed and to buld the application with the standard mvn package command. The app can then be started with

java -jar hpoworkbench-gui/target/HpoWorkbench.jar

Download current release

We are working on releasing native apps for Windows and Mac.

hpoworkbench's People

Contributors

cmungall avatar ielis avatar kingmanzhang avatar pnrobinson avatar

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Watchers

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Forkers

cmungall enriquea haoziyeung richeytastic 790675356 hekselman baiyide hugoguillen

hpoworkbench's Issues

Mondo integration

Here is a plan for Mondo parsing:
monarch-initiative/phenol#23
Prior to this, I would split the phenotype and the disease data into two separate tabs
I would show the OMIM and Orpha annotations that correspond to any given Mondo term.

No HPO terms present after downloading

I do the download:

image

After this completes there is no visual indication anything had downloaded, the screen looks like this:

image

I put 'abnormal' in the search box, click GO, nothing....

I also tried loading the annotations too

log:

~/repos/HPOworkbench(master) $ java -jar hpowbgui/target/hpowbgui-0.0.3-SNAPSHOT.jar 
[JavaFX Application Thread] TRACE (MainController.java:93) - Created HpoWorkench user directory at /Users/cjm/.hpoworkbench
Jan 03, 2018 8:54:22 AM javafx.fxml.FXMLLoader$ValueElement processValue
WARNING: Loading FXML document with JavaFX API of version 8.0.111 by JavaFX runtime of version 8.0.66
[JavaFX Application Thread] TRACE (MainController.java:198) - initialize
ERROR - 2018-01-03 08:54:23 - Unable to find HPO file at /Users/cjm/.hpoworkbench/hp.obo
[JavaFX Application Thread] ERROR (MainController.java:202) - Need to initialize ontology before we can start the application.
[JavaFX Application Thread] DEBUG (Downloader.java:72) - setLocalFilepath for download to: /Users/cjm/.hpoworkbench/hp.obo
[Thread-6] DEBUG (Downloader.java:89) - [INFO] Downloading: "https://raw.githubusercontent.com/obophenotype/human-phenotype-ontology/master/hp.obo"
[Thread-6] TRACE (Downloader.java:99) - URL host: raw.githubusercontent.com
 reader available=0
[Thread-6] TRACE (Downloader.java:100) - LocalFilePath: /Users/cjm/.hpoworkbench/hp.obo
[Thread-6] TRACE (Downloader.java:107) - Size of file to be downloaded: 5738327
[Thread-6] INFO  (Downloader.java:119) - Successful download from https://raw.githubusercontent.com/obophenotype/human-phenotype-ontology/master/hp.obo: 5738327(5738327) bytes read.
[JavaFX Application Thread] TRACE (MainController.java:129) - Successfully downloaded hpo to /Users/cjm/.hpoworkbench
[JavaFX Application Thread] DEBUG (Downloader.java:72) - setLocalFilepath for download to: /Users/cjm/.hpoworkbench/hp.obo
[Thread-8] DEBUG (Downloader.java:89) - [INFO] Downloading: "https://raw.githubusercontent.com/obophenotype/human-phenotype-ontology/master/hp.obo"
[Thread-8] TRACE (Downloader.java:99) - URL host: raw.githubusercontent.com
 reader available=0
[Thread-8] TRACE (Downloader.java:100) - LocalFilePath: /Users/cjm/.hpoworkbench/hp.obo
[Thread-8] TRACE (Downloader.java:107) - Size of file to be downloaded: 5738327
[Thread-8] INFO  (Downloader.java:119) - Successful download from https://raw.githubusercontent.com/obophenotype/human-phenotype-ontology/master/hp.obo: 5738327(5738327) bytes read.
[JavaFX Application Thread] TRACE (MainController.java:129) - Successfully downloaded hpo to /Users/cjm/.hpoworkbench

[JavaFX Application Thread] DEBUG (Downloader.java:72) - setLocalFilepath for download to: /Users/cjm/.hpoworkbench/phenotype_annotation.tab
[Thread-10] DEBUG (Downloader.java:89) - [INFO] Downloading: "http://compbio.charite.de/jenkins/job/hpo.annotations/lastStableBuild/artifact/misc/phenotype_annotation.tab"
[Thread-10] TRACE (Downloader.java:99) - URL host: compbio.charite.de
 reader available=840
[Thread-10] TRACE (Downloader.java:100) - LocalFilePath: /Users/cjm/.hpoworkbench/phenotype_annotation.tab
[Thread-10] TRACE (Downloader.java:107) - Size of file to be downloaded: 18896952
[Thread-10] INFO  (Downloader.java:119) - Successful download from http://compbio.charite.de/jenkins/job/hpo.annotations/lastStableBuild/artifact/misc/phenotype_annotation.tab: 18896952(18896952) bytes read.
[JavaFX Application Thread] TRACE (MainController.java:168) - Successfully downloaded phenotype_annotation.tab to /Users/cjm/.hpoworkbench
[JavaFX Application Thread] DEBUG (Downloader.java:72) - setLocalFilepath for download to: /Users/cjm/.hpoworkbench/hp.obo
[Thread-12] DEBUG (Downloader.java:89) - [INFO] Downloading: "https://raw.githubusercontent.com/obophenotype/human-phenotype-ontology/master/hp.obo"
[Thread-12] TRACE (Downloader.java:99) - URL host: raw.githubusercontent.com
 reader available=0
[Thread-12] TRACE (Downloader.java:100) - LocalFilePath: /Users/cjm/.hpoworkbench/hp.obo
[Thread-12] TRACE (Downloader.java:107) - Size of file to be downloaded: 5738327
[Thread-12] INFO  (Downloader.java:119) - Successful download from https://raw.githubusercontent.com/obophenotype/human-phenotype-ontology/master/hp.obo: 5738327(5738327) bytes read.
[JavaFX Application Thread] TRACE (MainController.java:129) - Successfully downloaded hpo to /Users/cjm/.hpoworkbench

files:

$ ls -alt ~/.hpoworkbench/
total 48120
-rw-r--r--    1 cjm  staff   5738327 Jan  3 08:59 hp.obo
-rw-r--r--    1 cjm  staff  18896952 Jan  3 08:57 phenotype_annotation.tab
drwxr-xr-x    4 cjm  staff       136 Jan  3 08:56 .
drwxr-xr-x+ 411 cjm  staff     13974 Jan  3 08:54 ..

without a term selected I can't export, e.g.

[JavaFX Application Thread] ERROR (MainController.java:379) - Select a term before exporting hierarchical summary TODO show error window

Modifiers-- transfer these from the Description to the new Modifier field

MODIFIER:EPISODIC;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > QUADRIPLEGIA, EPISODIC
MODIFIER:PROGRESSIVE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > COMMUNICATING HYDROCEPHALUS, PROGRESSIVE
MODIFIER:MILD;OMIM-CS:HEAD AND NECK_EYES > NYSTAGMUS, MILD
MODIFIER:MILD;OMIM-CS:HEAD AND NECK_EYES > PHOTOPHOBIA, MILD
MODIFIER:MILD;OMIM-CS:HEAD AND NECK_FACE > FACIAL ASYMMETRY (MILD)
MODIFIER:MILD;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > COGNITIVE IMPAIRMENT, MILD
MODIFIER:SEVERE;OMIM-CS:SKIN, NAILS, HAIR_NAILS > ONYCHODYSTROPHY, SEVERE
MODIFIER:MILD;OMIM-CS:MUSCLE, SOFT TISSUE > HYPOTONIA, MILD
MODIFIER:SEVERE;OMIM-CS:GENITOURINARY_INTERNAL GENITALIA, FEMALE > DYSMENORRHEA, SEVERE
MODIFIER:MODERATE;OMIM-CS:skeletalpelvis > FEMORAL HYPOPLASIA, MODERATE
MODIFIER:MILD;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > SPEECH DELAY, MILD
MODIFIER:MILD;OMIM-CS:HEAD AND NECK_FACE > FACIAL MUSCLE WEAKNESS, MILD
MODIFIER:MILD;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > EXTRAPYRAMIDAL SIGNS, MILD
MODIFIER:MILD;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > TREMOR, MILD
MODIFIER:MODERATE;OMIM-CS:headandneckeyes > MYOPIA, MODERATE
MODIFIER:PROXIMAL;OMIM-CS:MUSCLE, SOFT TISSUE > MUSCLE ATROPHY, PROXIMAL
MODIFIER:DISTAL;OMIM-CS:MUSCLE, SOFT TISSUE > MUSCLE WEAKNESS, DISTAL
MODIFIER:PROXIMAL;OMIM-CS:MUSCLE, SOFT TISSUE > MUSCLE WEAKNESS, PROXIMAL
MODIFIER:MILD;OMIM-CS:SKELETAL_SPINE > LUMBAR LORDOSIS, MILD
MODIFIER:MILD;OMIM-CS:HEMATOLOGY > ANEMIA, MILD
MODIFIER:CHRONIC;OMIM-CS:GENITOURINARY_KIDNEYS > NEPHRITIS, CHRONIC
MODIFIER:DISTAL;OMIM-CS:LIMBS > ARTHROGRYPOSIS, DISTAL
MODIFIER:DISTAL;OMIM-CS:JOINTS > ARTHROGRYPOSIS, DISTAL
MODIFIER:SEVERE;OMIM-CS:GROWTH_OTHER > POSTNATAL GROWTH RETARDATION, SEVERE
MODIFIER:BILATERAL;OMIM-CS:SKELETAL_FEET > BROAD HALLUX, BILATERAL
MODIFIER:BILATERAL;OMIM-CS:SKELETAL_FEET > BROAD HALLUX, BILATERAL
MODIFIER:MILD;OMIM-CS:HEAD AND NECK_FACE > MIDFACE HYPOPLASIA, MILD
MODIFIER:MILD;OMIM-CS:HEAD AND NECK_MOUTH > MICROGNATHIA, MILD
MODIFIER:MILD;OMIM-CS:CARDIOVASCULAR_HEART > AORTIC STENOSIS, MILD
MODIFIER:SEVERE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > DELAYED PSYCHOMOTOR DEVELOPMENT, SEVERE
MODIFIER:MILD;OMIM-CS:HEAD AND NECK_FACE > MIDFACE HYPOPLASIA, MILD
MODIFIER:SEVERE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > DELAYED PSYCHOMOTOR DEVELOPMENT, SEVERE
MODIFIER:MILD;OMIM-CS:CHEST_RIBS, STERNUM, CLAVICLES, AND SCAPULAE > PECTUS EXCAVATUM, MILD
MODIFIER:EPISODIC;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > ENCEPHALOPATHY, EPISODIC
MODIFIER:MILD;OMIM-CS:LABORATORY ABNORMALITIES > METHYLMALONIC ACIDURIA, MILD
MODIFIER:PROFOUND;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > DEVELOPMENTAL DELAY, PROFOUND
MODIFIER:PROGRESSIVE;OMIM-CS:SKELETAL > JOINT STIFFNESS, PROGRESSIVE
MODIFIER:PROGRESSIVE;OMIM-CS:SKELETAL > CONTRACTURES, PROGRESSIVE
MODIFIER:SEVERE;OMIM-CS:RESPIRATORY > ABSENCE OF SPONTANEOUS RESPIRATION (SEVERE FORM)
MODIFIER:SEVERE;OMIM-CS:SKELETAL > ARTHROGRYPOSIS (SEVERE FORM)
MODIFIER:SEVERE;OMIM-CS:SKELETAL_FEET > TOE CONTRACTURES, SEVERE
MODIFIER:SEVERE;OMIM-CS:SKELETAL_HANDS > FINGER CONTRACTURES, SEVERE
MODIFIER:MILD;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > PSYCHOMOTOR RETARDATION, MILD
MODIFIER:SEVERE;OMIM-CS:SKEL > SEVERE OSTEOPETROSIS
MODIFIER:SEVERE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > GLOBAL DEVELOPMENTAL DELAY, SEVERE
MODIFIER:SEVERE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > DEVELOPMENTAL DELAY, SEVERE
MODIFIER:EPISODIC;OMIM-CS:RESPIRATORY > APNEA, EPISODIC
MODIFIER:EPISODIC;OMIM-CS:HEME > EPISODIC NEUTROPENIA
MODIFIER:MILD;OMIM-CS:HEAD AND NECK_MOUTH > PROGNATHISM, MILD
MODIFIER:SEVERE;OMIM-CS:HEAD AND NECK_MOUTH > DENTAL CARIES, SEVERE
MODIFIER:MILD;OMIM-CS:HEAD AND NECK_FACE > FACIAL DYSMORPHISM, MILD
MODIFIER:PROGRESSIVE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > NEURODEGENERATION, PROGRESSIVE
MODIFIER:MILD;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > COGNITIVE IMPAIRMENT, MILD
MODIFIER:SEVERE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > MENTAL RETARDATION, SEVERE
MODIFIER:PROGRESSIVE;OMIM-CS:MUSCLE, SOFT TISSUE > MUSCLE WASTING, PROGRESSIVE
MODIFIER:SEVERE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > DELAYED PSYCHOMOTOR DEVELOPMENT, SEVERE
MODIFIER:REFRACTORY;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > SEIZURES, REFRACTORY
MODIFIER:SEVERE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > DELAYED PSYCHOMOTOR DEVELOPMENT, SEVERE
MODIFIER:SEVERE;OMIM-CS:SKIN, NAILS, HAIR_SKIN > PALMOPLANTAR HYPERKERATOSIS, SEVERE
MODIFIER:MILD;OMIM-CS:GENITOURINARY_EXTERNAL GENITALIA, MALE > HYPOSPADIAS, MILD
MODIFIER:MILD;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > SEIZURES, MILD
MODIFIER:SEVERE;OMIM-CS:MUSCLE, SOFT TISSUE > MUSCULAR HYPOTONIA, SEVERE
MODIFIER:PROFOUND;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > MENTAL RETARDATION, PROFOUND
MODIFIER:PROGRESSIVE;OMIM-CS:NEUROLOGIC_PERIPHERAL NERVOUS SYSTEM > PERIPHERAL NEUROPATHY, PROGRESSIVE
MODIFIER:SEVERE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > MENTAL RETARDATION, SEVERE
MODIFIER:CHRONIC;OMIM-CS:ABDOMEN_LIVER > CHRONIC HEPATITIS
MODIFIER:PROFOUND;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > MENTAL RETARDATION, SEVERE, PROFOUND
MODIFIER:MILD;OMIM-CS:GROWTH_HEIGHT > DWARFISM, MILD
MODIFIER:PROXIMAL;OMIM-CS:SKELETAL_LIMBS > SHORT RADII, PROXIMAL
MODIFIER:SEVERE;OMIM-CS:MUSCLE, SOFT TISSUE > MUSCLE WEAKNESS, SEVERE
MODIFIER:MILD;OMIM-CS:NEUROLOGIC_BEHAVIORAL/PSYCHIATRIC MANIFESTATIONS > HYPERACTIVE BEHAVIOR, MILD
MODIFIER:MILD;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > DEVELOPMENTAL DELAY, MILD
MODIFIER:PROGRESSIVE;OMIM-CS:HEAD AND NECK_EYES > VISUAL LOSS, PROGRESSIVE
MODIFIER:EPISODIC;OMIM-CS:MUSCLE, SOFT TISSUE > WEAKNESS, EPISODIC
MODIFIER:BILATERAL;OMIM-CS:GENITOURINARY_KIDNEYS > HYDRONEPHROSIS, BILATERAL
MODIFIER:DISTAL;OMIM-CS:SKELETAL_HANDS > ARTHROGRYPOSIS, DISTAL
MODIFIER:SEVERE;OMIM-CS:GROWTH_OTHER > FAILURE TO THRIVE, SEVERE
MODIFIER:MILD;OMIM-CS:HEAD AND NECK_EYES > SYNOPHRYS, MILD
MODIFIER:MILD;OMIM-CS:SKIN, NAILS, HAIR_HAIR > SYNOPHRYS, MILD
MODIFIER:MILD;OMIM-CS:MUSCLE, SOFT TISSUE > DISTAL MUSCLE WASTING, MILD
MODIFIER:MILD;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > LOWER LIMB SPASTICITY, MILD
MODIFIER:SEVERE;OMIM-CS:HEAD AND NECK_EYES > NIGHT BLINDNESS, SEVERE
MODIFIER:MODERATE;OMIM-CS:SKIN, NAILS, HAIR_SKIN > PARAKERATOSIS, MODERATE
MODIFIER:MODERATE;OMIM-CS:skinnailshairskinhistology > ACANTHOSIS, MODERATE
MODIFIER:PROFOUND;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > PSYCHOMOTOR RETARDATION, PROFOUND
MODIFIER:MILD;OMIM-CS:CARDIOVASCULAR_VASCULAR > PULMONARY HYPERTENSION, MILD
MODIFIER:PROGRESSIVE;OMIM-CS:HEAD AND NECK_EYES > CORNEAL CLOUDING, PROGRESSIVE
MODIFIER:RECURRENT;OMIM-CS:metabolicfeatures > FEVER, RECURRENT
MODIFIER:PROGRESSIVE;OMIM-CS:SKIN, NAILS, HAIR_HAIR > HAIR LOSS, PROGRESSIVE
MODIFIER:GENERALIZED;OMIM-CS:skinnailshairskin > VITILIGO, GENERALIZED
MODIFIER:BILATERAL;OMIM-CS:HEAD AND NECK_EARS > CONDUCTIVE HEARING LOSS, BILATERAL
MODIFIER:SEVERE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > DELAYED PSYCHOMOTOR DEVELOPMENT, SEVERE
MODIFIER:SEVERE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > MENTAL RETARDATION, SEVERE
MODIFIER:PROGRESSIVE;OMIM-CS:SKELETAL > PROGRESSIVE OSTEOPENIA
MODIFIER:RECURRENT;OMIM-CS:HEAD AND NECK_NOSE > RHINITIS, RECURRENT
MODIFIER:PROFOUND;OMIM-CS:HEAD AND NECK_EARS > DEAFNESS, PROFOUND
MODIFIER:PROFOUND;OMIM-CS:HEAD AND NECK_EARS > DEAFNESS, PROFOUND
MODIFIER:EPISODIC;OMIM-CS:HEMATOLOGY > HEMOLYTIC ANEMIA, EPISODIC
MODIFIER:PROGRESSIVE;OMIM-CS:neurologiccentralnervoussystem > MEMORY LOSS, PROGRESSIVE
MODIFIER:REFRACTORY;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > SEIZURES, REFRACTORY
MODIFIER:SEVERE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > DELAYED PSYCHOMOTOR DEVELOPMENT, SEVERE
MODIFIER:MILD;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > INTELLECTUAL IMPAIRMENT, MILD
MODIFIER:DISTAL;OMIM-CS:MUSCLE, SOFT TISSUE > MUSCLE WEAKNESS, PROGRESSIVE, DISTAL
MODIFIER:PROXIMAL;OMIM-CS:MUSCLE, SOFT TISSUE > MUSCLE WEAKNESS, PROGRESSIVE, PROXIMAL
MODIFIER:MILD;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > COGNITIVE IMPAIRMENT, MILD
MODIFIER:MILD;OMIM-CS:HEAD AND NECK_EYES > EXOPHTHALMOS, MILD
MODIFIER:BILATERAL;OMIM-CS:HEAD AND NECK_EYES > PTOSIS, BILATERAL
MODIFIER:MILD;OMIM-CS:HEAD AND NECK_EARS > HEARING LOSS, MILD
MODIFIER:MILD;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > DEVELOPMENTAL DELAY, MILD
MODIFIER:PROFOUND;OMIM-CS:HEAD AND NECK_EARS > HEARING LOSS, SENSORINEURAL, PROFOUND
MODIFIER:PROGRESSIVE;OMIM-CS:HEAD AND NECK_EYES > LOSS OF VISUAL ACUITY, PROGRESSIVE
MODIFIER:PROGRESSIVE;OMIM-CS:HEAD AND NECK_EYES > MACULAR ATROPHY, PROGRESSIVE
MODIFIER:PROGRESSIVE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > CEREBRAL WHITE MATTER ATROPHY, PROGRESSIVE
MODIFIER:EPISODIC;OMIM-CS:ABDOMEN_GASTROINTESTINAL > INTESTINAL EDEMA, EPISODIC
MODIFIER:EPISODIC;OMIM-CS:ABDOMEN_GASTROINTESTINAL > VOMITING, EPISODIC
MODIFIER:EPISODIC;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > DYSKINESIA, EPISODIC
MODIFIER:REFRACTORY;OMIM-CS:neurologiccentralnervoussystem > SEIZURES, REFRACTORY
MODIFIER:EPISODIC;OMIM-CS:ABDOMEN > ABDOMINAL PAIN, EPISODIC
MODIFIER:EPISODIC;OMIM-CS:HEAD AND NECK_MOUTH > APHTHOUS ULCERS, EPISODIC
MODIFIER:EPISODIC;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > HEADACHE, EPISODIC
MODIFIER:EPISODIC;OMIM-CS:SKIN, NAILS, HAIR_SKIN > URTICARIA, EPISODIC
MODIFIER:PROGRESSIVE;OMIM-CS:SKELETAL_HANDS > CAMPTODACTYLY (PROGRESSIVE)
MODIFIER:SEVERE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > MENTAL RETARDATION, SEVERE
MODIFIER:SEVERE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > PSYCHOMOTOR DELAY, SEVERE
MODIFIER:MODERATE;OMIM-CS:skinnailshairskinhistology > ACANTHOSIS, MODERATE
MODIFIER:PROGRESSIVE;OMIM-CS:MUSCLE, SOFT TISSUE > MUSCLE ATROPHY, PROGRESSIVE
MODIFIER:BILATERAL;OMIM-CS:HEAD AND NECK_EYES > REDUCED VISUAL ACUITY, BILATERAL
MODIFIER:SEVERE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > DELAYED MOTOR DEVELOPMENT, SEVERE
MODIFIER:MILD;OMIM-CS:MUSCLE, SOFT TISSUE > MUSCLE WEAKNESS, PROXIMAL, MILD
MODIFIER:EPISODIC;OMIM-CS:MUSCLE, SOFT TISSUE > MUSCLE WEAKNESS, EPISODIC
MODIFIER:PROXIMAL;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > LOWER LIMB MUSCLE WEAKNESS, PROXIMAL
MODIFIER:SEVERE;OMIM-CS:GROWTH_OTHER > POSTNATAL GROWTH RETARDATION, SEVERE
MODIFIER:PROGRESSIVE;OMIM-CS:skinnailshairhair > HAIR LOSS, PROGRESSIVE
MODIFIER:MILD;OMIM-CS:SKIN, NAILS, HAIR_SKIN > EPIDERMOLYTIC HYPERKERATOSIS, MILD
MODIFIER:RECURRENT;OMIM-CS:ABDOMEN_GASTROINTESTINAL > RECURRENT VOMITING
MODIFIER:SEVERE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > CEREBRAL ATROPHY, DIFFUSE, SEVERE
MODIFIER:SEVERE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > DEVELOPMENTAL RETARDATION, SEVERE
MODIFIER:SEVERE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > DELAYED SPEECH DEVELOPMENT, SEVERE
MODIFIER:SEVERE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > CEREBELLAR ATROPHY, SEVERE
MODIFIER:PROFOUND;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > DEVELOPMENTAL DELAY, PROFOUND
MODIFIER:PROGRESSIVE;OMIM-CS:HEAD AND NECK_EYES > PERIPAPILLARY CHORIORETINAL ATROPHY, PROGRESSIVE
MODIFIER:MILD;OMIM-CS:GENITOURINARY_EXTERNAL GENITALIA, FEMALE > HYPOPLASTIC LABIA MAJORA, MILD
MODIFIER:MILD;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > PSYCHOMOTOR RETARDATION, MILD
MODIFIER:GENERALIZED;OMIM-CS:SKELETAL_LIMBS > JOINT LAXITY, GENERALIZED
MODIFIER:MILD;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > CLUMSINESS (MILD)
MODIFIER:MILD;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > HYPOTONIA (MILD)
MODIFIER:SEVERE;OMIM-CS:HEAD AND NECK_HEAD > MICROCEPHALY, PROFOUND (AT LEAST 10 SD BELOW MEAN)
MODIFIER:RECURRENT;OMIM-CS:SKIN, NAILS, HAIR_SKIN > CELLULITIS, RECURRENT
MODIFIER:MILD;OMIM-CS:GENITOURINARY_EXTERNAL GENITALIA, MALE > HYPOSPADIAS, MILD
MODIFIER:MILD;OMIM-CS:RESPIRATORY_LUNG > PULMONARY HYPOPLASIA, MILD
MODIFIER:EPISODIC;OMIM-CS:HEAD AND NECK_EYES > VISION LOSS, EPISODIC
MODIFIER:PROGRESSIVE;OMIM-CS:IMMUNOLOGY > LYMPHOPENIA, PROGRESSIVE
MODIFIER:SEVERE;OMIM-CS:HEAD AND NECK_EYES > HIGH MYOPIA, SEVERE
MODIFIER:BILATERAL;OMIM-CS:HEAD AND NECK_EARS > PREAURICULAR SINUS, BILATERAL
MODIFIER:MILD;OMIM-CS:HEMATOLOGY > THROMBOCYTOPENIA, MILD
MODIFIER:MILD;OMIM-CS:HEAD AND NECK_EYES > BLEPHAROPHIMOSIS, MILD
MODIFIER:BILATERAL;OMIM-CS:HEAD AND NECK_EYES > CONGENITAL CATARACTS, BILATERAL
MODIFIER:PROFOUND;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > MENTAL RETARDATION, PROFOUND
MODIFIER:MILD;OMIM-CS:LABORATORY ABNORMALITIES > INCREASED SERUM CREATINE KINASE, MILD
MODIFIER:MILD;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > CEREBELLAR ATROPHY, MILD
MODIFIER:MODERATE;OMIM-CS:neurologiccentralnervoussystem > MOTOR DELAY, MODERATE
MODIFIER:MODERATE;OMIM-CS:neurologiccentralnervoussystem > MOTOR DELAY, MODERATE
MODIFIER:BILATERAL;OMIM-CS:HEAD AND NECK_MOUTH > CLEFT LIP, BILATERAL
MODIFIER:BILATERAL;OMIM-CS:HEAD AND NECK_MOUTH > CLEFT PALATE, BILATERAL
MODIFIER:EPISODIC;OMIM-CS:METABOLIC FEATURES > LACTIC ACIDOSIS, EPISODIC
MODIFIER:EPISODIC;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > DIZZINESS, EPISODIC
MODIFIER:MILD;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > TRUNCAL ATAXIA, MILD
MODIFIER:MILD;OMIM-CS:HEAD AND NECK_EYES > HYPERTELORISM, MILD
MODIFIER:MODERATE;OMIM-CS:HEAD AND NECK_EYES > NYSTAGMUS, MODERATE
MODIFIER:MILD;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > DELAYED PSYCHOMOTOR DEVELOPMENT, MILD
MODIFIER:SEVERE;OMIM-CS:SKELETAL_HANDS > BRACHYDACTYLY, SEVERE
MODIFIER:EPISODIC;OMIM-CS:RESPIRATORY > HYPERVENTILATION, EPISODIC
MODIFIER:REFRACTORY;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > SEIZURES, REFRACTORY
MODIFIER:SEVERE;OMIM-CS:HEAD AND NECK_HEAD > MICROCEPHALY (-12 TO -14.5 SD)
MODIFIER:PROGRESSIVE;OMIM-CS:HEAD AND NECK_EYES > VISUAL IMPAIRMENT, PROGRESSIVE
MODIFIER:SEVERE;OMIM-CS:MUSCLE, SOFT TISSUE > MUSCLE ATROPHY, DIFFUSE, SEVERE
MODIFIER:GENERALIZED;OMIM-CS:skinnailshairskin > LIVEDO RETICULARIS, GENERALIZED
MODIFIER:MILD;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > DYSMETRIA, MILD
MODIFIER:NONPROGRESSIVE;OMIM-CS:HEAD AND NECK_EYES > DECREASED VISUAL ACUITY, NONPROGRESSIVE
MODIFIER:MILD;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > COGNITIVE IMPAIRMENT, MILD
MODIFIER:SEVERE;OMIM-CS:SKELETAL_SPINE > KYPHOSCOLIOSIS, SEVERE
MODIFIER:EPISODIC;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > HEMIPLEGIA, EPISODIC
MODIFIER:EPISODIC;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > QUADRIPLEGIA, EPISODIC
MODIFIER:PROGRESSIVE;OMIM-CS:musclesofttissue > HYPOTONIA, PROGRESSIVE
MODIFIER:PROGRESSIVE;OMIM-CS:neurologiccentralnervoussystem > AREFLEXIA, PROGRESSIVE
MODIFIER:PROFOUND;OMIM-CS:HEAD AND NECK_EARS > SENSORINEURAL DEAFNESS, PROFOUND
MODIFIER:PROFOUND;OMIM-CS:musclesofttissue > HYPOTONIA, PROFOUND
MODIFIER:RECURRENT;OMIM-CS:HEAD AND NECK_NOSE > RHINITIS, RECURRENT
MODIFIER:PROGRESSIVE;OMIM-CS:musclesofttissue > HYPOTONIA, PROGRESSIVE
MODIFIER:CHRONIC;OMIM-CS:ABDOMEN_LIVER > HEPATITIS, CHRONIC
MODIFIER:EPISODIC;OMIM-CS:METABOLIC > HYPOGLYCEMIA, EPISODIC
MODIFIER:BILATERAL;OMIM-CS:HEAD AND NECK_EARS > HEARING LOSS, BILATERAL
MODIFIER:RECURRENT;OMIM-CS:HEAD AND NECK_NOSE > RHINITIS, RECURRENT
MODIFIER:PROFOUND;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > GLOBAL DEVELOPMENTAL DELAY, PROFOUND
MODIFIER:MILD;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > GLOBAL DEVELOPMENTAL DELAY, MILD
MODIFIER:MILD;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > COGNITIVE IMPAIRMENT, MILD
MODIFIER:SEVERE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > DELAYED PSYCHOMOTOR DEVELOPMENT, SEVERE
MODIFIER:MILD;OMIM-CS:HEMATOLOGY > PANCYTOPENIA, MILD
MODIFIER:SEVERE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > DELAYED DEVELOPMENT, SEVERE
MODIFIER:MODERATE;OMIM-CS:skinnailshairskinhistology > ACANTHOSIS, MODERATE
MODIFIER:MILD;OMIM-CS:SKIN, NAILS, HAIR_SKIN > HYPERKERATOSIS, MILD
MODIFIER:EPISODIC;OMIM-CS:RESPIRATORY > CENTRAL APNEA, EPISODIC
MODIFIER:EPISODIC;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > PAIN, EPISODIC
MODIFIER:REFRACTORY;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > SEIZURES, REFRACTORY
MODIFIER:MILD;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > DYSARTHRIA (MILD)
MODIFIER:MILD;OMIM-CS:MUSCLE, SOFT TISSUE > MUSCLE ATROPHY, MILD
MODIFIER:MILD;OMIM-CS:HEAD AND NECK_EYES > STRABISMUS, MILD
MODIFIER:MILD;OMIM-CS:SKELETAL_FEET > CAMPTODACTYLY, MILD
MODIFIER:PROGRESSIVE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > SPASTIC DIPLEGIA, PROGRESSIVE
MODIFIER:MILD;OMIM-CS:LABORATORY ABNORMALITIES > INCREASED SERUM CREATINE KINASE, MILD
MODIFIER:SEVERE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > CEREBRAL ATROPHY, SEVERE
MODIFIER:SEVERE;OMIM-CS:HEAD AND NECK_HEAD > MICROCEPHALY, SEVERE (-9 S.D.)
MODIFIER:MILD;OMIM-CS:CHEST_EXTERNAL FEATURES > FUNNEL CHEST, MILD
MODIFIER:MILD;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > DEVELOPMENTAL DELAY, MILD
MODIFIER:PROXIMAL;OMIM-CS:MUSCLE, SOFT TISSUE > MUSCLE WEAKNESS, PROXIMAL
MODIFIER:MILD;OMIM-CS:HEAD AND NECK_EYES > PTOSIS, MILD
MODIFIER:MILD;OMIM-CS:MUSCLE, SOFT TISSUE > MUSCLE WEAKNESS, LIMB-GIRDLE, MILD
MODIFIER:PROGRESSIVE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > NEURODEGENERATION, PROGRESSIVE
MODIFIER:SEVERE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > MENTAL RETARDATION, SEVERE
MODIFIER:SEVERE;OMIM-CS:SKELETAL_HANDS > SYNDACTYLY, SEVERE
MODIFIER:MILD;OMIM-CS:HEAD AND NECK_EYES > PHOTOPHOBIA, MILD
MODIFIER:SEVERE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > DELAYED PSYCHOMOTOR DEVELOPMENT, SEVERE
MODIFIER:MILD;OMIM-CS:CARDIOVASCULAR_HEART > CARDIOMYOPATHY, DILATED, MILD
MODIFIER:PROGRESSIVE;OMIM-CS:neurologiccentralnervoussystem > MENTAL DEFICIENCY, PROGRESSIVE
MODIFIER:MILD;OMIM-CS:SKELETAL_LIMBS > BROAD FEMORAL NECK, MILD
MODIFIER:MILD;OMIM-CS:SKELETAL_SPINE > ODONTOID HYPOPLASIA, MILD
MODIFIER:PROGRESSIVE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > ENCEPHALOPATHY, PROGRESSIVE
MODIFIER:SEVERE;OMIM-CS:HEMATOLOGY > ANEMIA, SEVERE
MODIFIER:SEVERE;OMIM-CS:CARDIOVASCULAR_HEART > CARDIOMYOPATHY, DILATED, SEVERE
MODIFIER:SEVERE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > PSYCHOMOTOR RETARDATION, SEVERE
MODIFIER:MILD;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > DELAYED MYELINATION, MILD
MODIFIER:DISTAL;OMIM-CS:NEUROLOGIC_PERIPHERAL NERVOUS SYSTEM > AREFLEXIA, DISTAL
MODIFIER:DISTAL;OMIM-CS:NEUROLOGIC_PERIPHERAL NERVOUS SYSTEM > HYPOREFLEXIA, DISTAL
MODIFIER:CHRONIC;OMIM-CS:HEAD AND NECK_FACE > SINUSITIS, CHRONIC
MODIFIER:MILD;OMIM-CS:CHEST_RIBS, STERNUM, CLAVICLES, AND SCAPULAE > SCAPULAR WINGING, MILD
MODIFIER:MILD;OMIM-CS:HEAD AND NECK_FACE > FACIAL WEAKNESS, MILD
MODIFIER:SEVERE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > PSYCHOMOTOR RETARDATION, SEVERE
MODIFIER:SEVERE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > MENTAL RETARDATION, SEVERE
MODIFIER:SEVERE;OMIM-CS:MUSCLE, SOFT TISSUE > MUSCLE WEAKNESS, SEVERE
MODIFIER:PROXIMAL;OMIM-CS:MUSCLE, SOFT TISSUE > MUSCLE WEAKNESS, PROXIMAL
MODIFIER:PROGRESSIVE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > COGNITIVE DECLINE, PROGRESSIVE
MODIFIER:MILD;OMIM-CS:LABORATORY ABNORMALITIES > INCREASED SERUM LACTATE (MILD)
MODIFIER:MILD;OMIM-CS:GROWTH_OTHER > MACROSOMIA, MILD
MODIFIER:MILD;OMIM-CS:HEAD AND NECK_HEAD > MACROCEPHALY, MILD
MODIFIER:SEVERE;OMIM-CS:GROWTH_OTHER > POSTNATAL GROWTH RETARDATION, SEVERE
MODIFIER:PROFOUND;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > PSYCHOMOTOR RETARDATION, PROFOUND
MODIFIER:RECURRENT;OMIM-CS:HEAD AND NECK_HEAD > SINUSITIS, RECURRENT
MODIFIER:RECURRENT;OMIM-CS:HEAD AND NECK_HEAD > SINUSITIS, RECURRENT
MODIFIER:EPISODIC;OMIM-CS:ABDOMEN_LIVER > ACUTE LIVER FAILURE, EPISODIC
MODIFIER:EPISODIC;OMIM-CS:LABORATORY ABNORMALITIES > ABNORMAL LIVER ENZYMES, EPISODIC
MODIFIER:EPISODIC;OMIM-CS:LABORATORY ABNORMALITIES > HYPERAMMONEMIA, EPISODIC
MODIFIER:EPISODIC;OMIM-CS:METABOLIC FEATURES > KETOACIDOSIS, EPISODIC
MODIFIER:EPISODIC;OMIM-CS:METABOLIC FEATURES > LACTIC ACIDOSIS, EPISODIC
MODIFIER:SEVERE;OMIM-CS:GROWTH_WEIGHT > OBESITY, SEVERE
MODIFIER:SEVERE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > PSYCHOMOTOR RETARDATION, SEVERE
MODIFIER:SEVERE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > GLOBAL DEVELOPMENTAL DELAY, SEVERE
MODIFIER:RECURRENT;OMIM-CS:HEAD AND NECK_HEAD > SINUSITIS, RECURRENT
MODIFIER:RECURRENT;OMIM-CS:HEAD AND NECK_NOSE > RHINITIS, RECURRENT
MODIFIER:RECURRENT;OMIM-CS:HEAD AND NECK_HEAD > SINUSITIS, RECURRENT
MODIFIER:PROGRESSIVE;OMIM-CS:HEAD AND NECK_EYES > VISUAL LOSS, PROGRESSIVE
MODIFIER:MODERATE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > INTELLECTUAL DISABILITY, MODERATE
MODIFIER:RECURRENT;OMIM-CS:HEAD AND NECK_HEAD > SINUSITIS, RECURRENT
MODIFIER:RECURRENT;OMIM-CS:HEAD AND NECK_NOSE > RHINITIS, RECURRENT
MODIFIER:RECURRENT;OMIM-CS:HEAD AND NECK_HEAD > SINUSITIS, RECURRENT
MODIFIER:RECURRENT;OMIM-CS:HEAD AND NECK_NOSE > RHINITIS, RECURRENT
MODIFIER:RECURRENT;OMIM-CS:HEAD AND NECK_HEAD > SINUSITIS, RECURRENT
MODIFIER:RECURRENT;OMIM-CS:HEAD AND NECK_NOSE > RHINITIS, RECURRENT
MODIFIER:PROGRESSIVE;OMIM-CS:MUSCLE, SOFT TISSUE > MUSCLE WEAKNESS, PROGRESSIVE
MODIFIER:BILATERAL;OMIM-CS:SKELETAL_FEET > TALIPES EQUINOVARUS, BILATERAL
MODIFIER:SEVERE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > SPEECH DELAY, SEVERE
MODIFIER:MILD;OMIM-CS:MUSCLE, SOFT TISSUE > MUSCLE WEAKNESS, MILD
MODIFIER:MILD;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > DELAYED MOTOR DEVELOPMENT, MILD
MODIFIER:BILATERAL;OMIM-CS:HEAD AND NECK_EARS > PREAURICULAR FISTULAS, BILATERAL
MODIFIER:PROGRESSIVE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > ENCEPHALOPATHY, PROGRESSIVE
MODIFIER:PROFOUND;OMIM-CS:neurologiccentralnervoussystem > DELAYED PSYCHOMOTOR DEVELOPMENT, PROFOUND
MODIFIER:MILD;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > INTELLECTUAL DISABILITY, MILD
MODIFIER:MILD;OMIM-CS:CHEST_EXTERNAL FEATURES > PECTUS EXCAVATUM, MILD
MODIFIER:MILD;OMIM-CS:HEAD AND NECK_FACE > RETROGNATHIA, MILD
MODIFIER:SEVERE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > DELAYED PSYCHOMOTOR DEVELOPMENT, SEVERE
MODIFIER:BILATERAL;OMIM-CS:HEAD AND NECK_EYES > CONGENITAL CATARACTS, BILATERAL
MODIFIER:PROGRESSIVE;OMIM-CS:HEAD AND NECK_EYES > OPTIC NERVE ATROPHY, PROGRESSIVE
MODIFIER:RECURRENT;OMIM-CS:METABOLIC FEATURES > FEVER, RECURRENT
MODIFIER:RECURRENT;OMIM-CS:HEAD AND NECK_FACE > SINUSITIS, RECURRENT
MODIFIER:SEVERE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > DELAYED PSYCHOMOTOR DEVELOPMENT, SEVERE
MODIFIER:GENERALIZED;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > SEIZURES, GENERALIZED
MODIFIER:EPISODIC;OMIM-CS:RESPIRATORY > TACHYPNEA, EPISODIC
MODIFIER:PROFOUND;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > DELAYED PSYCHOMOTOR DEVELOPMENT, PROFOUND
MODIFIER:SEVERE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > GLOBAL DEVELOPMENTAL DELAY, SEVERE
MODIFIER:SEVERE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > DELAYED PSYCHOMOTOR DEVELOPMENT, SEVERE
MODIFIER:PROFOUND;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > DELAYED PSYCHOMOTOR DEVELOPMENT, PROFOUND
MODIFIER:SEVERE;OMIM-CS:SKELETAL_SPINE > KYPHOSCOLIOSIS, SEVERE
MODIFIER:PROFOUND;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > DELAYED PSYCHOMOTOR DEVELOPMENT, PROFOUND
MODIFIER:SEVERE;OMIM-CS:CARDIOVASCULAR_VASCULAR > HYPERTENSION, SEVERE
MODIFIER:BILATERAL;OMIM-CS:ENDOCRINE FEATURES > ADRENAL HYPERPLASIA, BILATERAL
MODIFIER:PROFOUND;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > DELAYED PSYCHOMOTOR DEVELOPMENT, PROFOUND
MODIFIER:SEVERE;OMIM-CS:MUSCLE, SOFT TISSUE > MUSCLE WEAKNESS, SEVERE
MODIFIER:SEVERE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > AXIAL HYPOTONIA, SEVERE
MODIFIER:PROGRESSIVE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > CEREBELLAR ATROPHY, PROGRESSIVE
MODIFIER:PROGRESSIVE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > CEREBRAL ATROPHY, PROGRESSIVE
MODIFIER:SEVERE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > DELAYED PSYCHOMOTOR DEVELOPMENT, SEVERE
MODIFIER:PROFOUND;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > MENTAL RETARDATION, PROFOUND
MODIFIER:PROGRESSIVE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > SPASTIC QUADRIPLEGIA, PROGRESSIVE
MODIFIER:MILD;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > PONTINE HYPOPLASIA, MILD
MODIFIER:PROXIMAL;OMIM-CS:MUSCLE, SOFT TISSUE > MUSCLE WEAKNESS, PROXIMAL
MODIFIER:PROGRESSIVE;OMIM-CS:MUSCLE, SOFT TISSUE > MUSCLE WEAKNESS, PROGRESSIVE
MODIFIER:PROGRESSIVE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > ENCEPHALOPATHY, PROGRESSIVE
MODIFIER:SEVERE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > GLOBAL DEVELOPMENTAL DELAY, SEVERE
MODIFIER:SEVERE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > DELAYED DEVELOPMENT, SEVERE
MODIFIER:SEVERE;OMIM-CS:HEAD AND NECK_EYES > MYOPIA, SEVERE
MODIFIER:SEVERE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > INTELLECTUAL DISABILITY, SEVERE
MODIFIER:SEVERE;OMIM-CS:RESPIRATORY > RESPIRATORY INSUFFICIENCY, SEVERE
MODIFIER:RECURRENT;OMIM-CS:RESPIRATORY > LOWER RESPIRATORY TRACT INFECTIONS, RECURRENT
MODIFIER:CHRONIC;OMIM-CS:RESPIRATORY > RESPIRATORY INFECTIONS, RECURRENT, CHRONIC
MODIFIER:PROFOUND;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > DELAYED PSYCHOMOTOR DEVELOPMENT, PROFOUND
MODIFIER:MILD;OMIM-CS:SKIN, NAILS, HAIR_SKIN > HYPERKERATOSIS, MILD
MODIFIER:PROFOUND;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > DELAYED PSYCHOMOTOR DEVELOPMENT, PROFOUND
MODIFIER:EPISODIC;OMIM-CS:HEMATOLOGY > DISSEMINATED INTRAVASCULAR COAGULATION, EPISODIC
MODIFIER:EPISODIC;OMIM-CS:HEMATOLOGY > PANCYTOPENIA, EPISODIC
MODIFIER:EPISODIC;OMIM-CS:METABOLIC FEATURES > FEVER, EPISODIC
MODIFIER:EPISODIC;OMIM-CS:MUSCLE, SOFT TISSUE > MUSCLE WEAKNESS, EPISODIC
MODIFIER:EPISODIC;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > ATAXIA, EPISODIC
MODIFIER:EPISODIC;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > SLURRED SPEECH, EPISODIC
MODIFIER:MILD;OMIM-CS:HEAD AND NECK_EYES > PHOTOPHOBIA, MILD
MODIFIER:MILD;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > INTELLECTUAL DISABILITY, MILD
MODIFIER:SEVERE;OMIM-CS:MUSCLE, SOFT TISSUE > MUSCLE ATROPHY, SEVERE
MODIFIER:SEVERE;OMIM-CS:MUSCLE, SOFT TISSUE > MUSCLE WEAKNESS, SEVERE
MODIFIER:MILD;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > MENTAL RETARDATION, MILD
MODIFIER:PROXIMAL;OMIM-CS:MUSCLE, SOFT TISSUE > MUSCLE WEAKNESS, PROXIMAL
MODIFIER:MILD;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > COGNITIVE IMPAIRMENT, MILD
MODIFIER:SEVERE;OMIM-CS:METABOLIC FEATURES > KETOACIDOSIS, SEVERE
MODIFIER:MILD;OMIM-CS:HEAD AND NECK_EYES > UPSLANTING PALPEBRAL FISSURES, MILD
MODIFIER:MODERATE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > MENTAL RETARDATION, MODERATE
MODIFIER:EPISODIC;OMIM-CS:SKELETAL > ARTHRALGIA, EPISODIC
MODIFIER:MILD;OMIM-CS:HEAD AND NECK_EYES > OPHTHALMOPLEGIA, MILD
MODIFIER:MILD;OMIM-CS:LABORATORY ABNORMALITIES > INCREASED SERUM LACTATE, MILD
MODIFIER:MILD;OMIM-CS:LABORATORY ABNORMALITIES > INCREASED SERUM PYRUVATE, MILD
MODIFIER:MILD;OMIM-CS:HEAD AND NECK_FACE > DYSMORPHIC FACIAL FEATURES, MILD
MODIFIER:SEVERE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > DELAYED PSYCHOMOTOR DEVELOPMENT, SEVERE
MODIFIER:SEVERE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > DELAYED PSYCHOMOTOR DEVELOPMENT, SEVERE
MODIFIER:GENERALIZED;OMIM-CS:MUSCLE, SOFT TISSUE > MUSCLE WEAKNESS, GENERALIZED
MODIFIER:PROFOUND;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > DELAYED PSYCHOMOTOR DEVELOPMENT, PROFOUND
MODIFIER:BILATERAL;OMIM-CS:HEAD AND NECK_EYES > POSTERIOR SUBCAPSULAR CATARACT, BILATERAL
MODIFIER:MILD;OMIM-CS:CHEST_EXTERNAL FEATURES > PECTUS EXCAVATUM, MILD
MODIFIER:SEVERE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > CEREBELLAR ATROPHY, SEVERE
MODIFIER:PROFOUND;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > DELAYED PSYCHOMOTOR DEVELOPMENT, PROFOUND
MODIFIER:REFRACTORY;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > SEIZURES, REFRACTORY
MODIFIER:PROXIMAL;OMIM-CS:MUSCLE, SOFT TISSUE > MUSCLE WEAKNESS, PROXIMAL
MODIFIER:PROXIMAL;OMIM-CS:MUSCLE, SOFT TISSUE > MUSCLE WEAKNESS, PROXIMAL
MODIFIER:MILD;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > HYDROCEPHALY, MILD
MODIFIER:PROGRESSIVE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > CEREBELLAR ATROPHY, PROGRESSIVE
MODIFIER:SEVERE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > MENTAL RETARDATION, SEVERE
MODIFIER:PROGRESSIVE;OMIM-CS:neurologiccentralnervoussystem > ESSENTIAL TREMOR, PROGRESSIVE
MODIFIER:SEVERE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > DELAYED PSYCHOMOTOR DEVELOPMENT, SEVERE
MODIFIER:EPISODIC;OMIM-CS:RESPIRATORY > APNEA, EPISODIC
MODIFIER:MILD;OMIM-CS:MUSCLE > MUSCLE ATROPHY, MILD
MODIFIER:MILD;OMIM-CS:MUSCLE > MUSCLE WEAKNESS, PROXIMAL, MILD
MODIFIER:DISTAL;OMIM-CS:SKELETAL > ARTHROGRYPOSIS MULTIPLEX CONGENITA, DISTAL
MODIFIER:DISTAL;OMIM-CS:SKELETAL > ARTHROGRYPOSIS MULTIPLEX CONGENITA, DISTAL
MODIFIER:DISTAL;OMIM-CS:SKELETAL_LIMBS > CONTRACTURES, DISTAL
MODIFIER:MILD;OMIM-CS:HEAD AND NECK_EYES > PTOSIS, MILD
MODIFIER:EPISODIC;OMIM-CS:RESPIRATORY > RESPIRATORY INSUFFICIENCY, EPISODIC
MODIFIER:SEVERE;OMIM-CS:MUSCLE, SOFT TISSUE > GENERALIZED MUSCLE WEAKNESS, SEVERE
MODIFIER:EPISODIC;OMIM-CS:RESPIRATORY > RESPIRATORY INSUFFICIENCY, EPISODIC
MODIFIER:EPISODIC;OMIM-CS:RESPIRATORY > RESPIRATORY INSUFFICIENCY, EPISODIC
MODIFIER:EPISODIC;OMIM-CS:RESPIRATORY > RESPIRATORY INSUFFICIENCY, EPISODIC
MODIFIER:EPISODIC;OMIM-CS:RESPIRATORY > RESPIRATORY INSUFFICIENCY, EPISODIC
MODIFIER:MILD;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > DELAYED DEVELOPMENT, MILD
MODIFIER:PROGRESSIVE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > CEREBRAL ATROPHY, PROGRESSIVE
MODIFIER:PROFOUND;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > DELAYED PSYCHOMOTOR DEVELOPMENT, PROFOUND
MODIFIER:PROFOUND;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > DELAYED PSYCHOMOTOR DEVELOPMENT, PROFOUND
MODIFIER:REFRACTORY;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > SEIZURES, REFRACTORY
MODIFIER:REFRACTORY;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > SEIZURES, REFRACTORY
MODIFIER:PROGRESSIVE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > CEREBELLAR ATROPHY, PROGRESSIVE
MODIFIER:SEVERE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > DELAYED PSYCHOMOTOR DEVELOPMENT, SEVERE
MODIFIER:MILD;OMIM-CS:HEAD AND NECK_EYES > HYPERTELORISM, MILD
MODIFIER:MILD;OMIM-CS:HEAD AND NECK_EYES > HYPERTELORISM, MILD
MODIFIER:SEVERE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > DELAYED PSYCHOMOTOR DEVELOPMENT, SEVERE
MODIFIER:REFRACTORY;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > SEIZURES, REFRACTORY
MODIFIER:MILD;OMIM-CS:HEAD AND NECK_FACE > FACIAL ASYMMETRY, MILD
MODIFIER:SEVERE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > INTELLECTUAL DISABILITY, SEVERE
MODIFIER:SEVERE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > DELAYED PSYCHOMOTOR DEVELOPMENT, SEVERE
MODIFIER:SEVERE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > DELAYED PSYCHOMOTOR DEVELOPMENT, SEVERE
MODIFIER:SEVERE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > DELAYED PSYCHOMOTOR DEVELOPMENT, SEVERE
MODIFIER:MILD;OMIM-CS:LABORATORY ABNORMALITIES > HYPERAMMONEMIA, MILD
MODIFIER:MILD;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > INTELLECTUAL DISABILITY, MILD
MODIFIER:PROGRESSIVE;OMIM-CS:HEAD AND NECK_EYES > VITREOUS DETACHMENT, PROGRESSIVE
MODIFIER:PROGRESSIVE;OMIM-CS:HEAD AND NECK_EYES > EXTERNAL OPHTHALMOPLEGIA, PROGRESSIVE
MODIFIER:SEVERE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > DELAYED PSYCHOMOTOR DEVELOPMENT, SEVERE
MODIFIER:SEVERE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > INTELLECTUAL DISABILITY, SEVERE
MODIFIER:SEVERE;OMIM-CS:HEAD AND NECK_EYES > CATARACT, CONGENITAL, SEVERE
MODIFIER:SEVERE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > DELAYED PSYCHOMOTOR DEVELOPMENT, SEVERE
MODIFIER:MILD;OMIM-CS:HEMATOLOGY > LYMPHOPENIA, MILD
MODIFIER:PROGRESSIVE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > ATAXIA, PROGRESSIVE
MODIFIER:MILD;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > ATROPHY OF CEREBELLAR VERMIS, MILD
MODIFIER:BILATERAL;OMIM-CS:SKELETAL_PELVIS > ACETABULAR DYSPLASIA, BILATERAL
MODIFIER:PROGRESSIVE;OMIM-CS:HEMATOLOGY > BONE MARROW FAILURE, PROGRESSIVE
MODIFIER:MODERATE;OMIM-CS:HEAD AND NECK_EYES > OPTIC DISC PALLOR, MODERATE
MODIFIER:SEVERE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > MENTAL RETARDATION, SEVERE
MODIFIER:MILD;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > CEREBELLAR ATROPHY, MILD
MODIFIER:SEVERE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > DELAYED PSYCHOMOTOR DEVELOPMENT, SEVERE
MODIFIER:SEVERE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > DELAYED PSYCHOMOTOR DEVELOPMENT, SEVERE
MODIFIER:MILD
MODIFIER:SEVERE;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > INTELLECTUAL DISABILITY, SEVERE
MODIFIER:PROFOUND;OMIM-CS:MUSCLE, SOFT TISSUE > HYPOTONIA, PROFOUND
MODIFIER:PROFOUND;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > DELAYED PSYCHOMOTOR DEVELOPMENT, PROFOUND
MODIFIER:PROFOUND;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > INTELLECTUAL DISABILITY, PROFOUND
MODIFIER:PROFOUND;OMIM-CS:musclesofttissue > HYPOTONIA, PROFOUND
MODIFIER:MILD;OMIM-CS:HEAD AND NECK_EYES > PTOSIS, MILD
MODIFIER:MILD;OMIM-CS:SKELETAL_SPINE > THORACOLUMBAR SCOLIOSIS, MILD
MODIFIER:MILD;OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > HYPOTONIA, MILD
MODIFIER:PROGRESSIVE;OMIM-CS:abdomenliver > CHOLESTATIC LIVER DISEASE, PROGRESSIVE
MODIFIER:PROGRESSIVE;OMIM-CS:neurologiccentralnervoussystem > NEURODEGENERATION, PROGRESSIVE
MODIFIER:PROFOUND;OMIM-CS:neurologiccentralnervoussystem > GLOBAL DEVELOPMENTAL DELAY, PROFOUND
MODIFIER:REFRACTORY;OMIM-CS:neurologiccentralnervoussystem > SEIZURES, REFRACTORY
MODIFIER:RECURRENT;OMIM-CS:respiratorylung > ASPIRATION PNEUMONIA, RECURRENT
MODIFIER:PROGRESSIVE;OMIM-CS:growthother > GROWTH FAILURE, PROGRESSIVE
MODIFIER:REFRACTORY;OMIM-CS:neurologiccentralnervoussystem > SEIZURES, REFRACTORY
MODIFIER:PROFOUND;OMIM-CS:neurologiccentralnervoussystem > DELAYED PSYCHOMOTOR DEVELOPMENT, PROFOUND
MODIFIER:REFRACTORY;OMIM-CS:neurologiccentralnervoussystem > SEIZURES, REFRACTORY
MODIFIER:PROGRESSIVE;OMIM-CS:abdomenliver > LIVER FAILURE, PROGRESSIVE
MODIFIER:REFRACTORY;OMIM-CS:neurologiccentralnervoussystem > SEIZURES, REFRACTORY
MODIFIER:REFRACTORY;OMIM-CS:neurologiccentralnervoussystem > SEIZURES, REFRACTORY
MODIFIER:PROGRESSIVE;OMIM-CS:headandneckeyes > RETINAL DYSTROPHY, PROGRESSIVE
MODIFIER:PROFOUND;OMIM-CS:musclesofttissue > HYPOTONIA, PROFOUND
MODIFIER:REFRACTORY;OMIM-CS:neurologiccentralnervoussystem > SEIZURES, REFRACTORY
MODIFIER:GENERALIZED;OMIM-CS:neurologiccentralnervoussystem > DYSTONIA, GENERALIZED
MODIFIER:RECURRENT;OMIM-CS:respiratory > APNEA, RECURRENT
MODIFIER:PROGRESSIVE;OMIM-CS:headandneckeyes > REDUCED VISUAL ACUITY, PROGRESSIVE
MODIFIER:GENERALIZED;OMIM-CS:neurologiccentralnervoussystem > SEIZURES, GENERALIZED
MODIFIER:MODERATE;OMIM-CS:growthother > GROWTH RETARDATION, MODERATE
MODIFIER:REFRACTORY;OMIM-CS:neurologiccentralnervoussystem > SEIZURES, REFRACTORY
MODIFIER:PROGRESSIVE;OMIM-CS:skeletalspine > KYPHOSCOLIOSIS, PROGRESSIVE
MODIFIER:RECURRENT;OMIM-CS:abdomengastrointestinal > RECURRENT VOMITING

Unable to export to excel

Exporting to excel worked properly before but whith latest versions, process starts but no export file is generated.
In log file, logging stopped log entries in "creating excel" process:

2018-07-12 11:22:23,236 [JavaFX Application Thread] TRACE org.monarchinitiative.hpoworkbench.controller.HpoController - exporting to excel
2018-07-12 11:23:07,120 [JavaFX Application Thread] TRACE org.monarchinitiative.hpoworkbench.controller.HpoController - Setting path to LOINC Core Table file to C:\ExportedFiles\hpo.xlsx
2018-07-12 11:23:07,391 [JavaFX Application Thread] TRACE org.monarchinitiative.hpoworkbench.excel.Hpo2ExcelExporter - Creating excel

Regards

MONDO obo file

Die Workbench fordert den Nutzer auf, drei Dateien fรผr die Nutzung herunterzuladen, darunter auch die MONDO obo file. Wenn die Datei heruntergeladen wird, lรคsst sich die Workbench nutzen. Wenn die Workbench dann geschlossen wird und spรคter wieder geรถffnet werden soll, reagiert das Programm nicht. Die Workbench lรคsst sich nun nicht mehr รถffnen. Das Problem lรคsst sich nur dadurch lรถsen, dass die drei Dateien vom Computer vollstรคndig gelรถscht werden. Wenn dann die ersten beiden Dateien wieder gedownloaded werden, gibt es auch beim mehrmaligen Starten der Workbench keine Probleme. Sobald aber die MONDO obo file gedownloaded wird und die Workbench geschlossen wird, lรคsst sie sich danach nicht mehr รถffnen.

Cannot get this to run

HI, Iแธฟ very interested in HPOWorkbench, but cannot get it to run: The windows exe just wont start and does not seem to do anything (java 1.8.0144). The jar file under Ubuntu 16.04 reports "Error: Could not find or load main class org.monarchinitiative.hpoworkbench.Main".

During building from src with Maven i Get:

org.apache.maven.lifecycle.LifecycleExecutionException: Failed to execute goal org.apache.maven.plugins:maven-enforcer-plugin:1.4.1:enforce (enforce) on project HPOworkbench: Some Enforcer rules have failed. Look above for specific messages explaining why the rule failed.

I would appreciate some help with setting it up.

Unable to Download HPO annotations from HPOworkbench

Hello,

I want to use HPOworkbench for my research and I just downloaded the workbench v.1.6.1 today. However, I tried downloading HPO annotations from the edit tab for many times but nothing changes. Please find the screenshot below.

image

Could you please advise on how I can resolve this?

Thank you!
Sokanha

Import local hp obo file not working

image

I get:

image

First, it's not clear why it's complaining about the annot file when I'm refreshing the ont file

Second, the file is actually there:

$ ls -alt ~/.hpoworkbench/phenotype_annotation.tab 
-rw-r--r--  1 cjm  staff  18896952 Jan  3 08:57 /Users/cjm/.hpoworkbench/phenotype_annotation.tab

hierarchical summary

it seems to be stuck on my first choice Abnormal mitochondria in muscle tissue, and when I export it I only get one row / one level

Export ontology works (Parent field still blank)

Export hierachal summaryโ€œ

Die Funktion โ€žExport hierachal summaryโ€œ funktioniert meist beim ersten Versuch gut. Bei allen weiteren Versuchen mit einem anderen ausgewรคhlten Phรคnotyp erscheint allerdings immer eine Datei mit demselben Inhalt wie beim ersten Export. Wenn bspw. beim ersten Versuch โ€žAbnormal spermatogenesisโ€œ ausgewรคhlt wurde und die entsprechende Exceldatei erstellt wurde, wird im Folgenden immer dieselbe Datei erstellt, selbst, wenn danach ein anderer Phรคnotyp wie โ€žHypogonadismโ€œ gewรคhlt wurde. Das Problem besteht unabhรคngig von den ausgewรคhlten Phรคnotypen. Es lรคsst sich nur durch einen Neustart der Workbench lรถsen.

mode

When the user is in the disease mode and then clicks an HPO term in the tree view, the MODE is not switched to HPO browsing and the radio button remains set to disease.

suggestions for documentation

See obophenotype/human-phenotype-ontology#3369 (comment)

just added a new ticket via the workbench. Might I suggest some clarifications to the instructions, because I wasn't able to properly follow the instructions the first time. My suggestions are in italics.

Viewing annotated diseases
The diseases annotated to a given HPO term (including direct and implied annotations) can be viewed in the browser. If desired, users can limit the diseases to one of the databases, Orphanet, OMIM, or DECIPHER. To find the disease of interest, choose the radio button diseases in the upper left and use the autocomplete field to find the disease, and click on the GO button.

Suggesting new annotations
First navigate to a disease of interest as above. Then, click on the New annotation radio button in the upper left. Then use the autocomplete field or the HPO ontology hierarchy on the left to find the term you would like to propose as a new annotation for the disease. Then, click on the Suggest new annotation button on the bottom of the screen to open a new GitHub issue as above. Again, please modify the text to provide information to support the suggestion. You will need your GitHub ID and password to submit a new issue. Use the Report mistaken annotation if you have found an error in the annotations for some disease.

Unable to compile on Linux

Hi @pnrobinson,

I'm unable to compile the HPOWorkbench on Linux. I'm using maven v3.8.5.

I'm also using java version 17.0.3

openjdk 17.0.3 2022-04-19
OpenJDK Runtime Environment (build 17.0.3+7-Ubuntu-0ubuntu0.20.04.1)
OpenJDK 64-Bit Server VM (build 17.0.3+7-Ubuntu-0ubuntu0.20.04.1, mixed mode, sharing)

Here is the error report:

june-young@DESKTOP-PJI8A90:~/HPOworkbench$ mvn clean package
[INFO] Scanning for projects...
[WARNING]
[WARNING] Some problems were encountered while building the effective model for org.monarchinitiative.hpoworkbench:hpoworkbench-core:jar:2.1.4
[WARNING] 'version' contains an expression but should be a constant. @ org.monarchinitiative.hpoworkbench:hpoworkbench-core:${project.parent.version}, /home/june-young/HPOworkbench/hpoworkbench-core/pom.xml, line 10, column 14
[WARNING]
[WARNING] Some problems were encountered while building the effective model for org.monarchinitiative.hpoworkbench:hpoworkbench-cli:jar:2.1.4
[WARNING] 'version' contains an expression but should be a constant. @ org.monarchinitiative.hpoworkbench:hpoworkbench-cli:${project.parent.version}, /home/june-young/HPOworkbench/hpoworkbench-cli/pom.xml, line 9, column 14
[WARNING]
[WARNING] Some problems were encountered while building the effective model for org.monarchinitiative.hpoworkbench:hpoworkbench-gui:jar:2.1.4
[WARNING] 'version' contains an expression but should be a constant. @ org.monarchinitiative.hpoworkbench:hpoworkbench-gui:${project.parent.version}, /home/june-young/HPOworkbench/hpoworkbench-gui/pom.xml, line 13, column 14
[WARNING]
[WARNING] It is highly recommended to fix these problems because they threaten the stability of your build.
[WARNING]
[WARNING] For this reason, future Maven versions might no longer support building such malformed projects.
[WARNING]
[WARNING] The project org.monarchinitiative.hpoworkbench:hpoworkbench:pom:2.1.4 uses prerequisites which is only intended for maven-plugin projects but not for non maven-plugin projects. For such purposes you should use the maven-enforcer-plugin. See https://maven.apache.org/enforcer/enforcer-rules/requireMavenVersion.html
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO]
[INFO] HPOworkbench [pom]
[INFO] org.monarchinitiative.hpoworkbench:hpoworkbench-core [jar]
[INFO] org.monarchinitiative.hpoworkbench:hpoworkbench-cli [jar]
[INFO] hpoworkbench-gui [jar]
[INFO]
[INFO] ----------< org.monarchinitiative.hpoworkbench:hpoworkbench >-----------
[INFO] Building HPOworkbench 2.1.4 [1/4]
[INFO] --------------------------------[ pom ]---------------------------------
[INFO]
[INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ hpoworkbench ---
[INFO]
[INFO] --------< org.monarchinitiative.hpoworkbench:hpoworkbench-core >--------
[INFO] Building org.monarchinitiative.hpoworkbench:hpoworkbench-core 2.1.4 [2/4]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO]
[INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ hpoworkbench-core ---
[INFO] Deleting /home/june-young/HPOworkbench/hpoworkbench-core/target
[INFO]
[INFO] --- maven-resources-plugin:3.2.0:resources (default-resources) @ hpoworkbench-core ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Using 'UTF-8' encoding to copy filtered properties files.
[INFO] skip non existing resourceDirectory /home/june-young/HPOworkbench/hpoworkbench-core/src/main/resources
[INFO] skip non existing resourceDirectory /home/june-young/HPOworkbench/hpoworkbench-core/src/main/resources
[INFO]
[INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ hpoworkbench-core ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 19 source files to /home/june-young/HPOworkbench/hpoworkbench-core/target/classes
[INFO] /home/june-young/HPOworkbench/hpoworkbench-core/src/main/java/org/monarchinitiative/hpoworkbench/github/GitHubLabelRetriever.java: Some input files use unchecked or unsafe operations.
[INFO] /home/june-young/HPOworkbench/hpoworkbench-core/src/main/java/org/monarchinitiative/hpoworkbench/github/GitHubLabelRetriever.java: Recompile with -Xlint:unchecked for details.
[INFO]
[INFO] --- maven-resources-plugin:3.2.0:testResources (default-testResources) @ hpoworkbench-core ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Using 'UTF-8' encoding to copy filtered properties files.
[INFO] skip non existing resourceDirectory /home/june-young/HPOworkbench/hpoworkbench-core/src/test/resources
[INFO]
[INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ hpoworkbench-core ---
[INFO] No sources to compile
[INFO]
[INFO] --- maven-surefire-plugin:3.0.0-M5:test (default-test) @ hpoworkbench-core ---
[INFO] No tests to run.
[INFO]
[INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ hpoworkbench-core ---
[INFO] Building jar: /home/june-young/HPOworkbench/hpoworkbench-core/target/hpoworkbench-core-2.1.4.jar
[INFO]
[INFO] --------< org.monarchinitiative.hpoworkbench:hpoworkbench-cli >---------
[INFO] Building org.monarchinitiative.hpoworkbench:hpoworkbench-cli 2.1.4 [3/4]
[INFO] --------------------------------[ jar ]---------------------------------
[WARNING] The POM for org.phenopackets.phenotools:phenotools-converter:jar:0.0.2-SNAPSHOT is missing, no dependency information available
[WARNING] The POM for org.phenopackets.phenotools:phenotools-builder:jar:0.0.2-SNAPSHOT is missing, no dependency information available
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for HPOworkbench 2.1.4:
[INFO]
[INFO] HPOworkbench ....................................... SUCCESS [ 0.124 s]
[INFO] org.monarchinitiative.hpoworkbench:hpoworkbench-core SUCCESS [ 2.343 s]
[INFO] org.monarchinitiative.hpoworkbench:hpoworkbench-cli FAILURE [ 0.180 s]
[INFO] hpoworkbench-gui ................................... SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 2.835 s
[INFO] Finished at: 2022-05-31T14:50:39+09:00
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal on project hpoworkbench-cli: Could not resolve dependencies for project org.monarchinitiative.hpoworkbench:hpoworkbench-cli:jar:2.1.4: The following artifacts could not be resolved: org.phenopackets.phenotools:phenotools-converter:jar:0.0.2-SNAPSHOT, org.phenopackets.phenotools:phenotools-builder:jar:0.0.2-SNAPSHOT: Could not find artifact org.phenopackets.phenotools:phenotools-converter:jar:0.0.2-SNAPSHOT -> [Help 1]
[ERROR]
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR]
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/DependencyResolutionException
[ERROR]
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR] mvn -rf :hpoworkbench-cli

Any ideas?

Thanks!

June-Young

Send word summaries

Aortopathies
Vascular disease
Cardiomyopathies
Valvular disease
Electrical abnormalities
Congenital lesions
Other

The GUI of the application is crashing

Hello there,

I am interested in using the HPO workbench, however when i run the application, i get the following error message:
Exception in thread "JavaFX Application Thread" java.lang.RuntimeException: java.lang.reflect.InvocationTargetException at javafx.fxml/javafx.fxml.FXMLLoader$MethodHandler.invoke(FXMLLoader.java:1787) at javafx.fxml/javafx.fxml.FXMLLoader$ControllerMethodEventHandler.handle(FXMLLoader.java:1670) at javafx.base/com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at javafx.base/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:238) at javafx.base/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at javafx.base/com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at javafx.base/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at javafx.base/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at javafx.base/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at javafx.base/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at javafx.base/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at javafx.base/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at javafx.base/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at javafx.base/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at javafx.base/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at javafx.base/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at javafx.base/com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at javafx.base/com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.base/javafx.event.Event.fireEvent(Event.java:198) at javafx.graphics/javafx.scene.Node.fireEvent(Node.java:8865) at javafx.controls/javafx.scene.control.Button.fire(Button.java:200) at javafx.controls/com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:206) at javafx.controls/com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at javafx.base/com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:218)

This is the java version that I am using:
openjdk version "11.0.7" 2020-04-14 OpenJDK Runtime Environment (build 11.0.7+10-post-Ubuntu-2ubuntu218.04) OpenJDK 64-Bit Server VM (build 11.0.7+10-post-Ubuntu-2ubuntu218.04, mixed mode, sharing)

I resolved the issues with JavaFX by adding the following dependencies:
`
org.openjfx
javafx-controls
11

    <dependency>
        <groupId>org.openjfx</groupId>
        <artifactId>javafx-fxml</artifactId>
        <version>11</version>
    </dependency>

    <dependency>
        <groupId>org.openjfx</groupId>
        <artifactId>javafx-web</artifactId>
        <version>11</version>
    </dependency>`

Thanks for any suggestions !

Failed to invoke HPO workbench on Mac OS X 10.12.6

Hi there,

I am interested in using the HPO workbench, but when I tried to download the jar, I got the following error message:

bash$ java -jar ~/Downloads/HpoWorkbench.jar 
Error: Could not find or load main class org.monarchinitiative.hpoworkbench.Main
Caused by: java.lang.NoClassDefFoundError: javafx/application/Application

This is the version of java I have:

bash$ java -version
openjdk version "11.0.1" 2018-10-16
OpenJDK Runtime Environment 18.9 (build 11.0.1+13)
OpenJDK 64-Bit Server VM 18.9 (build 11.0.1+13, mixed mode)

hpoworkbench.settings

We should write the aplication.properties to the .hpoworkbench dir. Still we are not catching the mondo.obo.path

Covered buttons

  1. When opening the JAVA file one my computer, I cant see some of the buttons (on the bottom right), because they are covered the "All resources set!" message. It happens even when I try to resize the window.
  2. I can also see that some of the "check circles" don't have a description, but rather have "..." instead. Is this suppose to happen?
    Thanks in advance.

Download HPO annotations

Hi! Hope to use this tool :) I tried to start, but can't seem to be able to download the HPO annotations file. I think the problem is in the Charite's site which is down right now...
Any solutions?
Thanks, Idan.

Window

Where can I find windows version of HPOworkbench?
Thanks

Unable to compile on Linux

Hi @pnrobinson,

I'm unable to compile the HPOWorkbench on Linux. I'm using maven v3.6.2.

Here is the error report:

mvn clean package
[INFO] Scanning for projects...
Downloading from central: https://repo.maven.apache.org/maven2/org/springframework/boot/spring-boot-starter-parent/2.5.1/spring-boot-starter-parent-2.5.1.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/springframework/boot/spring-boot-starter-parent/2.5.1/spring-boot-starter-parent-2.5.1.pom (8.6 kB at 25 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/springframework/boot/spring-boot-dependencies/2.5.1/spring-boot-dependencies-2.5.1.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/springframework/boot/spring-boot-dependencies/2.5.1/spring-boot-dependencies-2.5.1.pom (109 kB at 2.4 MB/s)
Downloading from central: https://repo.maven.apache.org/maven2/com/datastax/oss/java-driver-bom/4.11.1/java-driver-bom-4.11.1.pom
Downloaded from central: https://repo.maven.apache.org/maven2/com/datastax/oss/java-driver-bom/4.11.1/java-driver-bom-4.11.1.pom (4.1 kB at 207 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/io/dropwizard/metrics/metrics-bom/4.1.22/metrics-bom-4.1.22.pom
Downloaded from central: https://repo.maven.apache.org/maven2/io/dropwizard/metrics/metrics-bom/4.1.22/metrics-bom-4.1.22.pom (5.3 kB at 332 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/io/dropwizard/metrics/metrics-parent/4.1.22/metrics-parent-4.1.22.pom
Downloaded from central: https://repo.maven.apache.org/maven2/io/dropwizard/metrics/metrics-parent/4.1.22/metrics-parent-4.1.22.pom (17 kB at 948 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/groovy/groovy-bom/3.0.8/groovy-bom-3.0.8.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/codehaus/groovy/groovy-bom/3.0.8/groovy-bom-3.0.8.pom (26 kB at 825 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/infinispan/infinispan-bom/12.1.4.Final/infinispan-bom-12.1.4.Final.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/infinispan/infinispan-bom/12.1.4.Final/infinispan-bom-12.1.4.Final.pom (18 kB at 840 kB/s)
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[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.monarchinitiative.hpoworkbench:hpoworkbench-core:jar:2.1.1
[WARNING] 'version' contains an expression but should be a constant. @ org.monarchinitiative.hpoworkbench:hpoworkbench-core:${project.parent.version}, /nethome/oleraj/Apps/HPOWorkbench/HPOworkbench/hpoworkbench-core/pom.xml, line 10, column 14
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.monarchinitiative.hpoworkbench:hpoworkbench-cli:jar:2.1.1
[WARNING] 'version' contains an expression but should be a constant. @ org.monarchinitiative.hpoworkbench:hpoworkbench-cli:${project.parent.version}, /nethome/oleraj/Apps/HPOWorkbench/HPOworkbench/hpoworkbench-cli/pom.xml, line 9, column 14
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.monarchinitiative.hpoworkbench:hpoworkbench-gui:jar:2.1.1
[WARNING] 'version' contains an expression but should be a constant. @ org.monarchinitiative.hpoworkbench:hpoworkbench-gui:${project.parent.version}, /nethome/oleraj/Apps/HPOWorkbench/HPOworkbench/hpoworkbench-gui/pom.xml, line 13, column 14
[WARNING] 
[WARNING] It is highly recommended to fix these problems because they threaten the stability of your build.
[WARNING] 
[WARNING] For this reason, future Maven versions might no longer support building such malformed projects.
[WARNING] 
[WARNING] The project org.monarchinitiative.hpoworkbench:hpoworkbench:pom:2.1.1 uses prerequisites which is only intended for maven-plugin projects but not for non maven-plugin projects. For such purposes you should use the maven-enforcer-plugin. See https://maven.apache.org/enforcer/enforcer-rules/requireMavenVersion.html
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO] 
[INFO] HPOworkbench                                                       [pom]
[INFO] org.monarchinitiative.hpoworkbench:hpoworkbench-core               [jar]
[INFO] org.monarchinitiative.hpoworkbench:hpoworkbench-cli                [jar]
[INFO] hpoworkbench-gui                                                   [jar]
[INFO] 
[INFO] ----------< org.monarchinitiative.hpoworkbench:hpoworkbench >-----------
[INFO] Building HPOworkbench 2.1.1                                        [1/4]
[INFO] --------------------------------[ pom ]---------------------------------
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[snipped]


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Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/maven-shared-incremental/1.1/maven-shared-incremental-1.1.jar (14 kB at 137 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/ow2/asm/asm/6.2/asm-6.2.jar
Downloaded from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-java/0.9.10/plexus-java-0.9.10.jar (39 kB at 362 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/com/thoughtworks/qdox/qdox/2.0-M9/qdox-2.0-M9.jar
Downloaded from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-interpolation/1.14/plexus-interpolation-1.14.jar (61 kB at 550 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-compiler-api/2.8.4/plexus-compiler-api-2.8.4.jar
Downloaded from central: https://repo.maven.apache.org/maven2/org/sonatype/aether/aether-util/1.7/aether-util-1.7.jar (108 kB at 947 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-compiler-manager/2.8.4/plexus-compiler-manager-2.8.4.jar
Downloaded from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-compiler-manager/2.8.4/plexus-compiler-manager-2.8.4.jar (4.7 kB at 36 kB/s)
Downloaded from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-compiler-api/2.8.4/plexus-compiler-api-2.8.4.jar (27 kB at 205 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-compiler-javac/2.8.4/plexus-compiler-javac-2.8.4.jar
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-core/3.0/maven-core-3.0.jar (527 kB at 3.8 MB/s)
Downloaded from central: https://repo.maven.apache.org/maven2/org/ow2/asm/asm/6.2/asm-6.2.jar (111 kB at 783 kB/s)
Downloaded from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-compiler-javac/2.8.4/plexus-compiler-javac-2.8.4.jar (21 kB at 143 kB/s)
Downloaded from central: https://repo.maven.apache.org/maven2/com/thoughtworks/qdox/qdox/2.0-M9/qdox-2.0-M9.jar (317 kB at 1.9 MB/s)
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 21 source files to /nethome/oleraj/Apps/HPOWorkbench/HPOworkbench/hpoworkbench-core/target/classes
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for HPOworkbench 2.1.1:
[INFO] 
[INFO] HPOworkbench ....................................... SUCCESS [  0.997 s]
[INFO] org.monarchinitiative.hpoworkbench:hpoworkbench-core FAILURE [ 12.296 s]
[INFO] org.monarchinitiative.hpoworkbench:hpoworkbench-cli  SKIPPED
[INFO] hpoworkbench-gui ................................... SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  15.128 s
[INFO] Finished at: 2022-04-05T18:34:28-04:00
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.8.1:compile (default-compile) on project hpoworkbench-core: Fatal error compiling: invalid target release: 17 -> [Help 1]
[ERROR] 
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR] 
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException
[ERROR] 
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR]   mvn <args> -rf :hpoworkbench-core

After switching to develop branch and re-running, here is the output:

[INFO] Scanning for projects...
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.monarchinitiative.hpoworkbench:hpoworkbench-core:jar:2.1.1
[WARNING] 'version' contains an expression but should be a constant. @ org.monarchinitiative.hpoworkbench:hpoworkbench-core:${project.parent.version}, /nethome/oleraj/Apps/HPOWorkbench/HPOworkbench/HPOworkbench/hpoworkbench-core/pom.xml, line 10, column 14
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.monarchinitiative.hpoworkbench:hpoworkbench-cli:jar:2.1.1
[WARNING] 'version' contains an expression but should be a constant. @ org.monarchinitiative.hpoworkbench:hpoworkbench-cli:${project.parent.version}, /nethome/oleraj/Apps/HPOWorkbench/HPOworkbench/HPOworkbench/hpoworkbench-cli/pom.xml, line 9, column 14
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.monarchinitiative.hpoworkbench:hpoworkbench-gui:jar:2.1.1
[WARNING] 'version' contains an expression but should be a constant. @ org.monarchinitiative.hpoworkbench:hpoworkbench-gui:${project.parent.version}, /nethome/oleraj/Apps/HPOWorkbench/HPOworkbench/HPOworkbench/hpoworkbench-gui/pom.xml, line 13, column 14
[WARNING] 
[WARNING] It is highly recommended to fix these problems because they threaten the stability of your build.
[WARNING] 
[WARNING] For this reason, future Maven versions might no longer support building such malformed projects.
[WARNING] 
[WARNING] The project org.monarchinitiative.hpoworkbench:hpoworkbench:pom:2.1.1 uses prerequisites which is only intended for maven-plugin projects but not for non maven-plugin projects. For such purposes you should use the maven-enforcer-plugin. See https://maven.apache.org/enforcer/enforcer-rules/requireMavenVersion.html
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO] 
[INFO] HPOworkbench                                                       [pom]
[INFO] org.monarchinitiative.hpoworkbench:hpoworkbench-core               [jar]
[INFO] org.monarchinitiative.hpoworkbench:hpoworkbench-cli                [jar]
[INFO] hpoworkbench-gui                                                   [jar]
[INFO] 
[INFO] ----------< org.monarchinitiative.hpoworkbench:hpoworkbench >-----------
[INFO] Building HPOworkbench 2.1.1                                        [1/4]
[INFO] --------------------------------[ pom ]---------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ hpoworkbench ---
[INFO] 
[INFO] --------< org.monarchinitiative.hpoworkbench:hpoworkbench-core >--------
[INFO] Building org.monarchinitiative.hpoworkbench:hpoworkbench-core 2.1.1 [2/4]
[INFO] --------------------------------[ jar ]---------------------------------
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/poi/poi-ooxml/5.2.2/poi-ooxml-5.2.2.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/poi/poi-ooxml/5.2.2/poi-ooxml-5.2.2.pom (6.3 kB at 18 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/poi/poi/5.2.2/poi-5.2.2.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/poi/poi/5.2.2/poi-5.2.2.pom (3.5 kB at 184 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/commons-io/commons-io/2.11.0/commons-io-2.11.0.pom
Downloaded from central: https://repo.maven.apache.org/maven2/commons-io/commons-io/2.11.0/commons-io-2.11.0.pom (20 kB at 897 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/poi/poi-ooxml-lite/5.2.2/poi-ooxml-lite-5.2.2.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/poi/poi-ooxml-lite/5.2.2/poi-ooxml-lite-5.2.2.pom (2.6 kB at 173 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/xmlbeans/xmlbeans/5.0.3/xmlbeans-5.0.3.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/xmlbeans/xmlbeans/5.0.3/xmlbeans-5.0.3.pom (4.6 kB at 288 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/commons/commons-compress/1.21/commons-compress-1.21.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/commons/commons-compress/1.21/commons-compress-1.21.pom (20 kB at 505 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/com/github/virtuald/curvesapi/1.07/curvesapi-1.07.pom
Downloaded from central: https://repo.maven.apache.org/maven2/com/github/virtuald/curvesapi/1.07/curvesapi-1.07.pom (4.4 kB at 258 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/poi/poi-ooxml/5.2.2/poi-ooxml-5.2.2.jar
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/xmlbeans/xmlbeans/5.0.3/xmlbeans-5.0.3.jar
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/commons/commons-compress/1.21/commons-compress-1.21.jar
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/poi/poi-ooxml-lite/5.2.2/poi-ooxml-lite-5.2.2.jar
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/poi/poi/5.2.2/poi-5.2.2.jar
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/xmlbeans/xmlbeans/5.0.3/xmlbeans-5.0.3.jar (2.2 MB at 7.9 MB/s)
Downloading from central: https://repo.maven.apache.org/maven2/commons-io/commons-io/2.11.0/commons-io-2.11.0.jar
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/commons/commons-compress/1.21/commons-compress-1.21.jar (1.0 MB at 3.3 MB/s)
Downloading from central: https://repo.maven.apache.org/maven2/com/github/virtuald/curvesapi/1.07/curvesapi-1.07.jar
Downloaded from central: https://repo.maven.apache.org/maven2/com/github/virtuald/curvesapi/1.07/curvesapi-1.07.jar (112 kB at 278 kB/s)
Downloaded from central: https://repo.maven.apache.org/maven2/commons-io/commons-io/2.11.0/commons-io-2.11.0.jar (327 kB at 788 kB/s)
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/poi/poi/5.2.2/poi-5.2.2.jar (2.9 MB at 6.8 MB/s)
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/poi/poi-ooxml/5.2.2/poi-ooxml-5.2.2.jar (2.0 MB at 4.4 MB/s)
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/poi/poi-ooxml-lite/5.2.2/poi-ooxml-lite-5.2.2.jar (5.8 MB at 12 MB/s)
[INFO] 
[INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ hpoworkbench-core ---
[INFO] Deleting /nethome/oleraj/Apps/HPOWorkbench/HPOworkbench/HPOworkbench/hpoworkbench-core/target
[INFO] 
[INFO] --- maven-resources-plugin:3.2.0:resources (default-resources) @ hpoworkbench-core ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Using 'UTF-8' encoding to copy filtered properties files.
[INFO] skip non existing resourceDirectory /nethome/oleraj/Apps/HPOWorkbench/HPOworkbench/HPOworkbench/hpoworkbench-core/src/main/resources
[INFO] skip non existing resourceDirectory /nethome/oleraj/Apps/HPOWorkbench/HPOworkbench/HPOworkbench/hpoworkbench-core/src/main/resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ hpoworkbench-core ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 21 source files to /nethome/oleraj/Apps/HPOWorkbench/HPOworkbench/HPOworkbench/hpoworkbench-core/target/classes
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for HPOworkbench 2.1.1:
[INFO] 
[INFO] HPOworkbench ....................................... SUCCESS [  0.156 s]
[INFO] org.monarchinitiative.hpoworkbench:hpoworkbench-core FAILURE [  2.028 s]
[INFO] org.monarchinitiative.hpoworkbench:hpoworkbench-cli  SKIPPED
[INFO] hpoworkbench-gui ................................... SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  2.443 s
[INFO] Finished at: 2022-04-05T18:54:14-04:00
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.8.1:compile (default-compile) on project hpoworkbench-core: Fatal error compiling: invalid target release: 17 -> [Help 1]
[ERROR] 
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR] 
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException
[ERROR] 
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR]   mvn <args> -rf :hpoworkbench-core

Note that I don't have any experience with compiling Java code, so this could be a very simple error.

Any ideas?

Thanks!

Andrew

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